If they go to SF (hopefully instead of LA), finish line: Alcatraz Island!!!
As grand as Alcatraz is, I don't think it would work. It would be like last season, the winner would be dictated by whoever gets the first boat. If you place the final memory taskon the island, it wouldn't work either as there would be a very short run to the finish line.
Treasure Island and Yerba Buena Island is also another possibility. They'd be able to run around the islands.
As for flights out of Manila, the only direct flights I believe are to Honolulu, SF, and LA on Philippine Airlines. Honolulu is only Tuesday, Thursday and Saturdays, but it arrives in the morning. SF's flight arrives in the evening. And there are two daily flights to LAX, one arriving in the morning and the other in the evening.
Of course, they could also connect through other cities, like Beijing, Seoul or Tokyo that could get them into SF in the morning.