While most of the Okinawa islands belong to the subtropical climate, technically Yaeyama Islands belong to the tropical rainforest climate which results in the winter temperature being 2-4 Celsius degrees higher than on Okinawa Island and the other islands in the northern part of the Okinawa archipelago. Even in January and February, the average high temperature is 21°C (70°F), making the area a popular winter getaway, although it's often cloudy and windy due to the winter monsoon which makes it a bit too cool for sunbathing. Spring, around March and April, is an excellent time to visit. The rainy season starts early in May and continues until June. Unlike the rainy season in mainland Japan, it rains neither everyday nor all day long in Yaeyama Islands. Summer in Yaeyama Islands is hot and humid but still one of the peak visiting seasons, while September brings a succession of fierce typhoons. October and November are again good times to visit.
The Yaeyama Islands are a long way from anywhere.
The main airport of the Yaeyama Islands is on Ishigaki Island, and in the wake of the new airport opening on March 7, 2013, there have been major changes. Frequent flights from/to Naha (Okinawa Island) continue to be available as before, but the two long-time operators JTA and ANA have begun to see competition from newcomers Skymark and Peach, with the result that fares have come down substantially. The number of direct flights from/to various airports in central Japan has been increased. In the summer the new airport was officially recognized as international airport by Japan's Ministry of Land, Infrastructure, Transport and Tourism. Taiwan's TransAsia Airways, who for several years had been offering a limited charter service from/to Hualien, on the east coast of Taiwan (using propeller planes), as well as Mandarin Airlines are now providing a regularly scheduled summer service from/to Taipei. Hong Kong Express provides direct flights to Hong Kong. Negotiations are underway concerning direct flights from/to Korea, and a direct link to Russia is being considered as well.
Since Ryukyu Kaiun took the last passenger ferry out of service in 2007 and Arimura Sangyo went out of business altogether in 2008, there are no scheduled services to Taiwan, mainland Japan or islands outside the Yaeyama group. (Between late April and the end of October, Star Cruises  operates cruises from Keelung (near Taipei, Taiwan) to Okinawa Island, Miyako Island, and Ishigaki Island, but this is not a ferry service.)
There are frequent services from Ishigaki to Taketomi (just 10 minutes) and Iriomote (40 minutes). Regular boats also connect to the other islands, including the more remote Hateruma, and Yonaguni. The major operators are Anei Kankō and Yaeyama Kankō Ferry.
The Yaeyama Islands are about as off the beaten track as it gets in Japan, but each has its own distinct character. Ishigaki has some spectacular beaches and Iriomote is the only island in all Japan with authentic jungle and mangrove forests, while tiny Taketomi is known for its carefully maintained traditional Ryukyu village.
Thanks to the pristine coral reefs that surround practically all the islands, scuba diving is the number one sports activity. Ishigaki is known for its manta rays, while Yonaguni's star attractions are hammerhead sharks and underwater ruins.
Even with just a snorkel and mask, it's possible to see a good assortment of tropical fish and other marine life among the reefs just a short distance from the beaches. The best spots are probably Nakamoto Beach on Kuro Island and Star Sand Beach on Iriomote.
Yaeyama's best-known dish is the ubiquitous Yaeyama soba (八重山そば), which bears little resemblance to soba on the mainland: the Yaeyaman version consists of white wheat noodles in a mild pork-based stock, garnished with chunks of pork (sōki), some slices of fish cake and red ginger. Available everywhere for ¥400-500 a bowl.
The local beef is also renowned, although needless to say in Japan prime steaks don't come cheap. The tiny island of Kuro, in particular, is known for having more cows than people.
Some of the more exotic local fare on offer includes snake soup and mimigā, a salad of pork ear, cucumber and vinegar.
As elsewhere in Okinawa the tipple of choice is awamori, the best known local brand being Yaesen (八重泉), but Yonaguni is also known for its deadly 60° hanazake. In addition to the ubiquitous Orion beer, Ishigaki also houses a microbrewery.
Yaeyama poses no health risks apart from those found elsewhere in Okinawa. Use plenty of suntan lotion and don't insert your hands into holes in trees that make suspicious hissing sounds. One should, however, take care NOT to snorkel where there are posted warnings of the indigenous jellyfishes. These areas are usually clearly marked. Also, when scuba diving be aware that on the reefs the highly venomous Crown-of-Thorns seastar does exist, though the local diving service operators actively eliminate them when found as that species of seastar seriously damages the reefs and is extremely dangerous to humans.
The Yaeyama islands have over 200 utaki (御嶽, Japanese pronunciation: "otake"), known in the local language as ogan or on, which are sacred sites (places for venerating the gods). By order of the Japanese government, those "on" pertaining to villages (some of which only survive in the form of city sections now) as well as other more official "on" were outfitted with "torii" (鳥居)- Japanese shrine (神社, "jinja") gates - after the annexation of the Ryukyu kingdom (today's Okinawa Prefecture), but there are subsequently still many that don't have such gates but are instead marked off in other ways, for example, with low stone walls and Japanese signage. Please don't venture inside.
The definitive reference to the islands is Nanzansha's Yaeyama Guide Book (やえやま GUIDE BOOK, ISBN 4876413886, Amazon.co.jp), but alas, the only words of English in this yearly-updated tome are in the title. Still, the maps and thorough listings are invaluable, particularly for the smaller islands. Available in better bookstores throughout Japan for ¥1200, and older copies can almost always be found sitting around in Yaeyaman lodgings.
The free Yaeyama Navi (八重山ナビ) pamphlet with large, detailed maps is also quite good, but the listings inside are limited to paid advertisements.
The ferry companies offer package tours to the islands and information is available at the ferry terminal though most of it is in Japanese.WikiPedia:Yaeyama Islands