We'll be in town, up from DC, on our honeymoon (you're asking why we'd come there for our honeymoon in August, aren't you?) and I booked brunch at Aquavit. Upon further Chow-investigation, it seems that may not be the best choice (overpriced and less than amazing).
Considering Prune, Deborah and Five Points as a replacement.
Five Points takes reservations for brunch, so I'd move on that if you don't want to wait! The line can get hairy.
My shortlist of best Sunday brunches in NYC where you can make reservations includes:
Balthazar (brioche French Toast and sour cream waffles, great bacon, great bread basket, wonderful vibe)
Five Points (amazing churros and pork dishes, lemon ricotta pancakes too, pretty space with the flowers and water and skylight and all)
their sister restaurant Cookshop (good pastries, awesome thick cut bacon, a little more hip and bustling)
Devin Tavern (awesome bloody marys and lobster grilled cheese sandwich, kind of big and Midwestern in feel -- psuedo cowboy)
Neptune Room (love the country breakfast, the lobster benedict, and the creme brulee french toast).
I would have no qualms taking out of town guests to any of those, and it's a little easier on the schedule if you can make reservations. I would also have suggested Ouest's upscale prix fixe brunch but I'm not entirely certain that they're doing it in the summer. The Cafe at Country is good, too, if you happen to be staying in the area (get the pastry basket and pork grits).
If you find yourself reservationless and hungry at 9:30am, head over to Prune or Clinton Street Baking Company. If you miss that window, you're looking for a long wait. Prune seems slightly better than Clinton Street these days, although the crowds fluctuate a bit in the summer. If you're near a Sarabeth's, I'd go there before 10am, too.
If I don't have a plan and it's before 10am, I might head over to Balthazar and brave the crowds since they don't start serving brunch until 10am. Or I'd walk over to the West Village and go to Blue Ribbon Bakery or Jane, maybe.
Mmmm, brunch. My favorite meal of the weekend.
Deborah is fantastic-- and a lot more under the radar than most other brunch places in the city. They take reservations, though the wait is never too long. You don't compromise anything in food, service, or atmosphere, just a lot more low-key experience. From there grab a coffee from Joe on Waverly and wander west to the pier off Christopher St. and enjoy some waterfront Manhattan.
(and if you end up at Deborah the duck hash is incredible)
Theres a little place in tribeca called Walkers, give it a go...
there is also the Ear inn not too far away from there a little more far west village...
these were my favorite haunts as a young man. Mind you these recommendations are comming 20+ years later from a now maine transplant....