This subject is very personal to me. From my own nightmare with this I recommend waiting, if possible, until the cat isn't in heat. It sounds like your vet and you communicate well. However, make sure your vet is expirienced and up to date before allowing surgery, especially if she is in heat. Here's what happened to me if you're interested.
Seven years ago I took 2 cats from a friend to keep them out of a shelter. Dusty, male, was nearly 3 and Karina, female, was nearly 2. She had never seen a vet and had severe allergies. My vet said to get the allergies under control first, then do the series of vaccination, then get her spayed.
Several weeks later I took her for her surgery. The vet asked if she was in heat. Based on her behavior, I informed him that she was coming out of a cycle, but couldn't be sure. When I picked her up later he was annoyed.I was told that she was in heat and her uterus was engorged and had nearly ruptured during the surgery, but she was ok.
It took her nearly a month to recover and they never told me to bring her for a follow up. Soon she began having heat cycles again. I had a bad feeling about that vet so we decided to wait until we had a new one. When we moved, we consulted our new vet. He said there must still be ovarian tissue and exploratory surgery would best be done by the original vet.
When we moved again (now it was a couple of years) our new vet was outstanding! He was the only vet on our military post and has tons of expirience with all kinds of problems. We trusted him and gave detailed history. He said that finding the leftover tissue could be difficult.
It took about 2 more years, loads of tears and frustration, and finally 2 exploratory surgeries by our outstanding vet to finaly get the 1 1/2 ovaries left in her. After the first surgery he told me that her insides were messed up from the first vet and he had to do some corrections. She is finally happy and healthy.
Most vets are competent. However, don't underestimate the risk of having this done while she is in heat. Make sure the vet is qualified to succesfully perform the surgery the first time.