If the doctor knows you well, it would not hurt to get a LOR from him. Your academic letters are most important but non-academic letters are common as supplements to your academic letters.
How it worked at my school was that at least 2 LORs were required from pre-req science professors. After that, I could get letters from humanities professors, volunteer work coordinators or doctors I shadowed (basically whomever I wanted). I managed to get 2 science letters and one each from the latter three mentioned. I thought this would help paint a diverse picture of me to an admissions committee.
Regarding whether to ask now or not - find out if your school's prehealth office or advisor will hold on to your LOR if you had it written now. This is how it worked at my school - I could have it sent to the prehealth office and they would hold on to it for up to 3 years. Ideally, you should ask for a letter when you feel the person writing it has had a chance to know you well and/or when an experience with the writer is ending and you are "freshest" in the writer's mind.
Hope this helps!