I just gave my son my 1999 f150 4x4 with stock wheels, and he wants to go bigger. He's looking at a 3" body lift for now, with 33" tires. What wheel size will fit? From what I have read, it looks like 16"-18" wheels have the most tire options, and I think it has the 5x135 lug pattern, but I'm not positive on that, but I really have no idea where to start. Any suggestions would be appreciated.

 

New or used? You will get different opinions but me personally, I like more tire, less wheel. Im running 16x10,s on 35,s.[98 Expedition with 3" BL and 2" spacers] You will have no issues with 33,s with a 3" BL.
Whatever your budget is will depend on the size/type of the wheels and tires. 5x135 bolt pattern is getting harder by the day to find in a "nice" wheel imo.
Go through the classifieds and take a look

 

Yes, your bolt pattern is 5x135mm. I'd go with a 10 inch wide wheel with 4.5 inches of backspacing. With a 3 inch body lift, 33x12.50's or 35x12.50's will fit and look fine. I agree on going with a 16 or 18 inch wheel.