I stayed in Malta for work for 6 months but was based in Sliema.
It depends on your price range as to where is good to stay.
For middle of the road 3.5 to 4 stars you're better off in Sliema, which is a 15 minute ferry ride or a 30 minute bus ride from Valetta.
[I recommend The Waterfront, it was my choice of hotel, right on the seafront, friendly comfortable and great food]
A good site to find hotels is -
http://www.holidays-malta.com/malta_page…
But don't book through them, they don't always pass on your details properly and although the hotel I booked through there was accomodating and found me a room you may not be so lucky!