I was in the same exact situation as you this past application cycle and didn't listen to my UG adviser when he suggested I get someone else from my M.A. My advice, get 2 or more letters if you can from your M.A. program and have your UG as a fourth OR ask him if he has the confidence to write you a STRONG letter of rec. Found out from inside sources that I was rejected from my first choice because one of my letters was not walk-on-water-glowing-in-the-dark strong. Luckily, I got into a top program.
Anyways, good luck and do your best!!