I'm putting a 36V 112 lbs MK trolling motor on my Nautic Star but here is the question. With the 150 Yamaha 4 stroke having its own battery plus the 3 for the trolling, do I need a 4 bank charger or will the Yamaha keep it's battery charged and only need a 3 bank for the trolling battery's? In the older boat I've had the motors never kept the battery's charged enough not to throw the charger on it.

If you already have a 3 bank you are probably ok. If buying a new one, go with a 4 bank. It depends a lot on how often you use your boat. If not every week then you'll need a charger for every battery.
Since I use my boat a lot, I don't have an on board charger for the cranking battery BUT, I do have a 1 amp pulse charger for it that keeps the plates clean. I've had good experiences with it.