There's nothing wrong in making a polite inquiry if those agents have had your work for three months -- unless each one has clearly posted on his/her website that his/her turnaround time is a minimum of six months ...
... even then, though, I would feel well within my rights to contact an agent -- because if one short/polite inquiry from me after 12 weeks is going to piss him/her off, well, then, I wouldn't want him/her to represent me!
And congratulations for having so many agents interested in reading your work! Way to GO!
BTW: If you cannot get an answer from all three at this point, then explain the situation to the new agent. While you wouldn't be able to offer him/her an exclusive, you could promise not to send the work out to any further agents -- as well as offer him/her an exclusive for the rest of the work (should he/she want to read further). I did that once, and the agent thought it was just fine.