I think better in Times New Roman
I started submitting samples of my manuscript, using Times New Roman, to agents at Writing conferences. None of them ever commented on the font. Nor did my agent, when I finally landed one, nor my editor at HarperCollins.
When I finally got around to asking them, they said either was fine, and I've submitted every revision using TNR. I think it's more important to have the correct margins, etc., than to worry about the font, unless you're submitting cold to publishing houses, and then you should follow their guidelines. Real agents don't seem to care that much.
No agent, no editor, is going to say, "This is a really great work, but it's printed in TNR, so I'm rejecting it." Even if it violates their guidelines, if the editor has it in her hand, she's going to look at the first paragraph before she tosses it. So if you're hook works...
For me, it's important to see the words on the page the way the reader will eventually see them, i.e., real italics, real underlines, and more densely packed text. When I tried to do that with Courrier, it just didn't work for me, but you might want to try it yourself, and see if you think better in a different font. After all, you can always change it before you submit.
Several members of my critique group submit in Courrier, but others use TNR, and we all get along, mostly, except for the constant arguments. (We've given up on the font argument).
I suggest you worry more about your hook, and your first five pages, than the font you using.