Nano tanks are just a small sized tank, i.e. 20 gallons. There is no "real" definition on what constitutes as a "nano tank", but in my opinion it would be something less than 45 gallons.
A nano tank doesn't have to be a reef tank, but many times the people who build the tanks seem to include everything needed to make the tank into a reef tank. Some examples of what I'm talking about are the "nano cube" and "biocube" tanks.
A large reef tank is a lot of work, whereas a small nano tank is still expensive and work, but it could end up costing a lot less to set up a nano over a 90 gallon reef.