First of all, put yourself in the gate agent's shoes. At the risk of offending almost everybody on this board, I'm going to say gate agents probably have the most difficult job in this business. They get it from all directions--pax, crew, and other company employees. The last thing they want is lip from an offline jumpseater who is riding for free.
As a frequent jumpseater, I've run into a few grumpy gate agents and I try to empathize with them. The worst was an ex-TWA agent working for AA in STL. He was just mad at the world and you didn't want to get in his field of fire.
Just be as nice and polite as you can be. Avoid confrontation at all cost--it makes both of you look bad. Remember, he/she controls your fate unless you can get to the Captain. Even then, you may have to deal with them again, so it doesn't behoove you to pi** them off. I pass out miniature candy bars to gate agents and sometimes crewmembers--just a way of saying "Thanks. I appreciate your effort."
At jetBlue we have an unrestricted jumpseat policy and will fill up the cabin and our 2 extra FA jumpseats with all the non-revs we can fit. Of course, with loads at 86%, we may not always be able to take as many as want to go. I've been left at the gate while an RJ with a check airman in the jumpseat pushed back with 10 empty seats in the back. It isn't fair, but those are the rules. I almost got bumped today when the Captain thought he already had too many jumpseaters.
The best thing for us all will be to continue to ask our jumpseat coordinators, companies, unions, etc. for expanded jumpseat authorizations to any empty cabin pax or FA jumpseat. Until we can get the cockpit jumpseat back, we need to do everything we can to accommodate our commuting buddies!
In the mean time, if you have a problem, get the details and report it to your jumpseat coordinator. They can pass the info to the other company rep. Let that company handle it in their own way. We had an incident early on in company where a Captain had denied one of us a ride for no good reason. He got a lot of heat from his peers who had discovered how easy it is for both pilots and FAs to jumpseat on jetBlue, and who didn't want to lose the privilege because of one jerk. The pilots from that company were very apologetic whenever they heard a jetBlue callsign on the radio for the next couple of months. It is in everybody's best interest to cooperate so everybody can get to work with minimum hassle, so let's all play nice and "share our toys in the sandbox!!"