I can recommend two: the first is Pan Pacific Travel (http://www.panpacifictravel.ph), which is one of the more well-known travel agencies in Manila. Their main office is in Binondo (Chinatown), but they also have offices in Ermita and Makati.

The second is Rajah Travel (http://www.rajahtravel.com), which is the travel agency of my parents. Their main office is in Ermita, but they also have an office in Makati.