I made a similar choice last summer (except the internship was at Abbott, and not Pfizer). I went with the internship, mostly because it was a sweet deal-- free hotel room for the duration of my internship, free breakfast and dinner everyday, and great pay on top of everything else. I think it was a great experience to see how research is done in industry (since I had only ever worked in academic labs before), and I was able to talk about the differences and what I learned from them during my medical school interviews.
I think either one can look great on a medical school application (or, at least, choosing Abbott didn't seem to hurt me). It depends on what you're interested in doing, and I think the pay is important to consider as well. Thanks to working at Abbott last summer, I've managed to save up enough money for med school (it's not much, but it IS ~$10k that I won't need to take out in loans, and every little bit helps).