The SEER rating is the effeciency of the air conditioner and the number of tons is the cooling capacity.
For the SEER rating, higher is better. A 3 ton 13 SEER unit and a 3 ton 16 SEER unit will both provide the same amount of cooling, but the 16 SEER unit will use less electricity and cost less to run in the long run. You want as high of a SEER value as you can get and pay attention here because you probably will have to be above a minimum level in order to qualify for energy credits.
The number of tons is a little more tricky. The higher the number here the more cooling power the unit will provide, so you might think that more is better, but that is definitely not the case. If you have a unit that's rated too high for your house then it will cool the house down very quickly and only run in short bursts. This will cause more temperature fluctuations and also higher humidity levels in the house making it feel warmer than it is. Since the AC dehumidifies the air as it runs ideally it should be running for longer intervals. However, getting a unit that's rated too low will cause the AC to run almost all the time and it will use too much electricity. Additionally it may not be able to cool your house properly on the hottest days.
There are some standard calculations that a good contractor will use to determine the proper size AC for your house based on your window size and your sun exposure and the size of your rooms... this can be a bit involved to figure out so some contractors will just guess without actually running the numbers. This can lead to an incorrectly sized unit. If you already have an air conditioner that you've been happy with, then your new one should be about the same size (number of tons), but have a much higher SEER rating. If you're getting quotes for a different size than you have now you should definitely ask them why they're quoting that size. It might just be because that's the one they have left over in the back of the shop.