There's a place called Brunos that's right at the bridge in Fronteras. Brunos is a marina/restaurant and is a good place to get your bearings from. I'd do something like check into Brunos, spend a day or two exploring and then perhaps move somewhere else. The good thing about Brunos is that it's right in town and all the cruisers tie their dingys to the dock so you will have a chance to meet everyone in the area. There are water taxis that will take you everywhere from the bridge.

The most active marina is Marios. they have rooms also. http://www.mayaparadise.com/brunosmarina/brunosmarina.asp
I would fly to Guatemala City, grab a bus to Fronteras (Rio Dulce 4 hours) and check into Brunos. From there you can get your bearings and find a better place, or not. Perhaps take a water taxi to Marios marina or other for dinner and check out the hotel at the marina. Fronteras is an interesting place. Dirty, hot and lots of people but it has a charm that I liked.

You could probably rent a small skiff and cruise around the river till you were tired of it.

Photo is a sample of the old farts hanging out for the season at Marios Marina. Lots of parties, games and drinking. A short water taxi ride from Fronteras