I must say I'm torn about this. On the one had, if this was a regular employer (and considering the age of most graduate students and the duration of the programs, I largely see graduate school as employment) I would definitely say it would be foolish not to negotiate, even if you are the only one. Employers will give you as little as they think they can; it's up to you to ask for more in this system. On the other hand, graduate schools are also obviously providing us with a service-- education and credentials. I just don't know.
Also, would you accept a funding offer that was only for 3 years?