What are your interests. Manila is not the most tourist friendly city as far as tourist attractions go - there just aren't that many. But there are a few, which I am sure you have googled already.
Manila is not the safest place in the world, but it isn't totally unsafe either - just take the usual precautions you would in any major city in Asia (outside of HKG and SIN). Additionally, don't wear jewelery or carry your bag carelessly as I have been told by several people that petty crime increased after the floods on the lead up to Christmas - nothing more than opportunistic, but just be a little extra careful.
Boracay is great if you want to get away to a nice beach (thanks for the reminder to book my next holiday in a month or so!). SEAIR is the only airline that flies from MNL to Caticlan (a 10min boat ride from Boracay). Other airlines now fly to Kalibo which is a 100min van ride to the boat, then 10min by boat to Boracay. This is because of the length of the runway at Caticlan (it was recently downgraded). It is more expensive to fly to Caticlan, but there is the extra cost of the van ride from Kalibo (P1,000 each way?).
There are plenty of places to stay in Boracay, no matter your budget. Check out tripadvisor.com for something in your price range. There is plenty of cheap food and drink available on the island (along with a supermarket and ATM). Take a good book or two and enjoy the clear water and awesome beach.
Depending on your budget and interests, Cebu can be an okay city to visit. There are some day tours from Manila, including the Taal Volcano (extinct) tour if that is what you fancy.