Either is fine. Go with the one that fits your schedule. As you've found, Nature Air has a wide variety of fares, some of which permit very little luggage. Sansa allows overages, but when they'l transport your excess baggage is subject to availability.
Both operate out of Juan Santamaria Airport (SJO): Sansa, all; Nature Air, most. Sansa has its small own terminal, about 100 yards from the main terminal; Nature Air's operations are inside the main terminal.
Nature Air still operates a couple of flights from the much smaller Tobias Bolaņos Airport (SYQ) which is much closer to the city, but that doesn't include the Tambor flights.
I would find a hotel close to the airport rather than going into San Jose because you'll have to be back early the next morning. SJO is about 30 minutes outside the city.