You've sent a batch of queries and a couple of manuscripts. You've waited.
And now you've gotten a response.
But your response came from agent #3, and you really wanted to hear back from agent #1 before making a choice. Can you tell agent #3 that you want to think about it, or is it first come, first serve?
Absolutely tell agent #3 that you need to think about the offer. And then send a notification to everyone else who has your manuscript that you've gotten an offer - to those whom you think would work better with you than #3, tell them you've had an offer and would like to hear back from them. To those whom you think agent #3 would be better than, tell them you've had an offer and thank them for their time, but let them know you're now off the market.
This is professional, this is polite, and this is acceptable. Telling an agent that you've had a prior offer and you're still considering them gets them to take a deeper look at your manuscript - but, they will be rushed, so don't try using this as a ploy to get read. A rushed agent is more likely to say "No" than one who has had enough time to mull.
On the other hand, if you don't tell the other agents that you're now engaged in conversation with #3, you risk wasting everyone's time. Agent #3 deserves to know that you've sent a batch of queries, and it's perfectly acceptable to take a little time to communicate with them. But if you wait too long, you risk #3 starting to think that you're unreliable. And if you don't e-mail #4 to tell them your manuscript already has an agent, then when #4 gives you a call and you say the manuscript is off the market, they'll be mad at you for wasting their time. The industry isn't that big. It's not a good idea to irritate an agent, not even if you don't think you'll be working with them. At the very least, that's unprofessional behavior.
So, yes, if you get the call - make a call (or e-mail.) Let the other agents you've contacted know you've spoken with one agent and gotten an offer, and let them know if you're still considering them, or if you're now off the market. And while "Nyah-nyah, they got me first!" might be satisfying, it really won't help your cause - a polite "Thanks for your time, but I've gotten an offer and am withdrawing my query/manuscript" will suffice.
Besides, next book might be more to Agent #4's taste. And I know you're already working on the next one, right?