With the advances in technology with motors, how safe would you say it is to buy a 2 year old Boat (2017 Z19-Merc 200 ProXS 117 hours).  Is it possible to pull motor logs to ensure the motor was broke in properly. Also has warranty until 2022.

Yes. The dealership can pull a printout 

The engine’s computer has all that data stored.

The dealership has a reputation to withhold whereas Joe Blow does not. I would think it would be “safer” to be a used boat from a dealer. 

Dealer or private sale you can get the stats from the motor at any shop that has the software to pull it.  The advantage to a dealer is that "if" something major goes wrong in a reasonable time after the sale, they are better equipped to handle it than a private seller.  If you are going to get regular service from the dealer you are buying the boat from, they will be much more receptive if you bought it there.  Downside is that normally you will pay a little more for a dealership boat vs a private seller.