Is it better to purchase 1password from agilebits website or the app store?
There are benefits to both sides:


The Mac App Store's 1Password has iCloud syncing whereas the AgileBits store distribution method can't include iCloud syncing since an app must be distributed through the Mac App Store to use such Apple services.
The AgileBits store's 1Password is updated more frequently since the updates don't have to go through Apple's approval system. This also means you can get beta updates that aren't on the Mac App Store due to Apple's guidelines on beta distribution.