We have six supermarkets in town including the two you mentioned. A lot has to do with where you're staying. Both Fresh Market (formerly Albertsons) and Park City Market (formerly Dan's) are in town at intersection of SR224 and SR248. Both are easily reached by free bus. The others are all out at the I-80 junction, but also easily reached especially Whole Foods and Smith's.
Personally, we shop at Smith's. If I'm in town, I'll choose Park City Market over Fresh Market. There's also the primary state liquor store in the same parking lot as Park City Market.
There are also some smaller stores but any of these will work for you.
Edited: 12:48 pm, January 28, 2013