I would suggest that you make reservations for the communal dinner at Museo Na Bolom. The food is home cooking and served family style; your dining companions will be interesting and eager to converse. It may be that you will eat with some of the Lacondon indigenous people who frequently stay at Na Bolom.
Go early enough--an hour or so before your dinner--to tour the captivating home/museum and have a drink on the terrace before your meal. Just remember that the food is not the main course here; it's the experience of the museum, the ambiance, and the chance to interact with a fascinating group of people.
Your hotel will be able to make the reservations for you, or you can call yourself.
Funny story...After reading up before our trip through Campeche and Chiapas in Spring of 2010 we definitely wanted to experience the dinner at Na Bolom. So, we went to the museum, went right to make a reservation and...as luck would have it...they had space for the four of us. My husband was not feeling great in the evening so my 2 kids and I went alone, not wanting to miss out on a once in a lifetime experience.
We arrived to find 3 places set at the HUMONGOUS table in the dining room. We were the only guests for the evening. We settled in by the fire and were waited on hand and foot all the while making up stories about the previous inhabitants and their spirits still roaming he grounds.
I'm pretty sure I'll get my wrist slapped for linking to the blog post about that evening but if you want to see it, I would be happy to share the link. It was an amazing experience even though it was not what we expected.
Several recommendations for your trip. We found the food to be very good and very reasonable, although not as amazing as Puebla and Oaxaca.
Our favoraite meal was at La Trattatoria Italiano. It took several tries to get in and would recommendation you have a reservations because it is tiny and was full everytime we walked by. Wonderful ravioli that changes daily. We sampled potato/gorganzola in sage butter and rabbit in rosemary butter. Sharing an appetizer, several glasses of wine, pasta, dessert, and coffee for $50 US with tip and tax! And no, we don't usualy look for italian food in Mexico!
Another endorsement would be for Normita's on Felipe Flores. Small local restaurant run by a family that made wonderful pozole. It was our first meal when we arrived and was a perfect start to out trip.
Try Tamales Dona Ame for great tamales. We meant to go to El Mercadito which was highly recommended by everyone (Moon Chiapas guide, New York Times Frugal Traveller and several locals), but never made it. The locals wait in line out the door.
One night we tried to go to La Paloma, but we were turned away by the hour long wait. Although many seem to like it we were told that the service is slow and the food uneven.
La Casa de Pan was described by my husband as "any port in a storm." Not great, but good. They were out of the Tamales Chiapanecos which we had come for so that probabaly took away from our experience. We had vegetarian enchiladas mole (it was a vegetarian restuarant).
We were there the week between Christmas and New Years so it was rather crowed and bustling. Couldn't get a table at Na Bolom as recommendaed by "crsitina" below, but visited the museum. Hope you have as good of a trip as we did!