I wouldnt put him as a reference. There must be someone else u can put..like a different colleague at work or another superior that u got along with. Use them instead of someone u didnt get along with..especially if u know they might not say nice things about u.

But i dont agree that u should leave the 3 months out of resume. Because its your first job, even 3 months shows u have at least done some work in a field that is related to a new job that u apply for. 3 months is still better than a fresh grad with 0 experience. BUT you must know how to leverage on that by giving lots of details about the things u have learnt in 3 months that makes u different from a fresh grad. Also make sure u have a damn good and reasonable reason for leaving, because u will definitely be asked why in every interview. If youre going to be honest and say its because u didnt get along with your boss, then be prepared to explain in great detail. If u think its too hard to explain and will look bad on u, then leave it out.