Make sure you look at both boats when they're clean, and in the sun. A clean boat makes a WORLD of difference over a dusty dirty boat. If it were me, I'd go for the big motor with expectations that I might be using a little elbow grease to make it look pretty. I wouldn't want a purple boat, no matter how nice of condition it was in. Will the guy selling these boats pay for a compression check/mechanical inspection or at least credit that cost towards the purchase price? If not, it would be worth the money to have a mechanic come tell you everything is in order with the drivetrain. Also, lake test them both, there might be vibrations or something on one that aren't present on the other. That will give you an indication on condition of prop shaft, strut, etc.
Don't take out a loan on a boat that you are not 100% sure it runs perfectly. Cosmetic stuff, while it won't look pretty, will still allow you to use the boat and get it into great condition over time. A boat that doesn't run or has tranny/vdrive issues will just sit around while you pay for the boat as well as mechanical costs.