A well-driven manual will get MUCH better real world mileage than the same car with the automatic.
Even with taller highway gearing, I'd get the manual unless close to 100% of your driving is on the highway.
Here's why -- manuals are "handicapped" on the EPA test:
http://ecomodder.com/forum/showthrea...ing-27416.html
Here's a 5mt vs automatic comparison (same car, similar ratings):
http://ecomodder.com/forum/showthrea...cra-30059.html
Here's another one, 5MT vs CVT (same car, CVT rated higher):
http://ecomodder.com/forum/showthrea...age-27384.html
Besides, a manual just makes the drive more enjoyable (yes, even in the city).