APMEX has the lower price and probably lower quality, the Mint has higher prices and perhaps better quality.
I would assume you are referencing the ATB 5 oz coins with 2010 dates. The reason for the price difference is that they are selling two different types of coins. The coins that the mint sells were minted in Philadelphia and carry a P mintmark, with a mintage of "only" 27,000. The coins have a satin, matte finish and are known as the "Collector Version". The coins sold by APMEX carry no mintmark, (I believe they are minted in philly also but i may be worng. It may be westpoint.) and have higher mintages. The 2010-no mintmark coins carry a mintage of 33,000 and 2011 and on carry unlimited mintages. These coins have a more proof like appearance and are known as the bullion or investor version. In short, the coins sold by the mint are more expensive because they have a lower mintage.
Thanks for clearing that up. I've been so hooked on 19th century coinage(like the capped bust as your avatar) I haven't even been keeping up with current coin events... So bullion people should just stick with APMEX and collectors with the Mint?
It's a matter of preference. I bought the first three mint versions, despite the outrageous premium over spot, hoping that the demand is there in the future and they will eventually go up in value. If you are buying the coins for silver, go with the APMEX. (I would recommend Silver American Eagles though over these...).