I plan to apply for Masters. I am currently working as a research intern at a reputed University in my currently. I was assigned a Ph.D. mentor on joining the project by the Professor. Ph.D. mentor guided me on a daily basis and has a better understanding of my work and abilities than the Professor. The professor has little knowledge about my capabilities and I'm afraid he'll give me a very weak LOR if at all he agrees to give. Is it advisable to get a LOR from my Ph.D. mentor considering she does not have an official University email address or the University letterhead?
Although it looks more professional to have a faculty email address on a letter of recommendation, it is not a must.
The person that you are asking might have left the university, and also they might not yet have started in another university. This would not prevent you from having the letter of recommendation.
It is not advisable to get a letter of recommendation, even for a masters program, from somebody who is still a graduate student. Letters from graduate students are generally given very little weight in admission to U.S. graduate schools, and there are good reasons for this. Graduate students cannot be relied on to have the experience to evaluate students skills, relative to other typical graduate school applicants, or necessarily to judge whether a student is ready to complete a program of graduate studies.
Whether the letter from the graduate student is on official letterhead is of very little importance in comparison.