There are road & river connections to Tarapoto, & buses from there to the Pacific coast.
If you want to take a trip to Pacaya-Samiria National Reserve, you're better off going to Lagunas by yourself and booking a trip from there. The only thing the tour agency in Yurimaguas will do for you is buying a ticket for a boat (only one way) and booking a tour in another agency based in Lagunas.
You can visit restaurant "Mil Sabores" near to plaza de armas church
There are a few hostals in the main town (around the Plaza da Armas). However, most boats allow you to stay overnight before the start of the journey, and for no extra charge.
Most travellers are looking for River Transportation. Agencies near the harbour provide Speed boats to Lagunas and other small villages along the Marañon River.
Lanchas to Iquitos leave every 2 to 3 days. These cargo and passenger ships take about 2,5 days to Iquitos, with several stops on small river communities including Lagunas (12 hours) and Nauta (2 days). The Lanchas stay in Yurimaguas to load cargo for 1-3 days and leave right after the last box of onions has come on board. Departure times therefore change rapidly. The people in the harbour including captains may lie to you, telling the boat leaves in some hours, to sell you a ticket (S/90 to S/100, buy only from the captain). But anyways, you can put up your hammock already and stay on board until the boat leaves for no extra charge. Be aware of hookers, trying to rent you a hammock for way to much money. They also try to help with putting up your hammock. Don't care about them. You can buy hammocks in centre town for 20 to 30 soles.
EDUARDO runs the ships with the best services, also chosen by many locals. The included food is simple but good. Don't forget to bring a plastic box and spoon to get your food (in centre town S/2 for a big one, the bigger, the more food you get). Showers and toilets run with river water. Be aware of theft on board, especially at nighttime, as there are no lockers or private areas. It is recommended to buy some extra fruits and enough drinking water in advance, but food vendors will also come on board at every stop. Once the boat leaves, just enjoy this relaxing days on board, spotting river dolphins, wonderful sunsets and lots of stars at night.
In order to organise the boat trip, it is a good idea to check Yacuruna - jungle amazon adventure. This cheap wooden family owned hostel is located right on the riverside, just some stairs downstairs from Plaza de armas. Winston, the owner knows precisely about the schedules of the Lanchas and can organise your whole boat trip, probably even cheaper than on your own. The terrace of this hostel is very nice for sunrises and dolphin spotting.