We stayed a couple of nights en route from the peninsula to Manuel Antonio, and it was a great decision. It's a lovely boutique hotel, with the rooms opening onto the pool, surrounded by quiet farmland. The staff are really friendly and helpful. If you aren't driving and want to go into Jaco, you get a free cab ride, or even better, you can order food in for an evening meal and eat on your terrace.
Breakfast was good, and it was lovely to sit outside and drink a coffee by the pool before having another dip..
I personally don't know why anyone would make a special trip to stay in Jaco city, as it seemed a bit plastic, but this is a great base for exploring the area or breaking a journey. Beautiful.