Hi Colwyn,
the best hotels overlooking the harbour, that is Grand Harbour, the principal harbour in Malta also known in shipspotting.com as Valletta harbour are the British Hotel and the Grand Harbour Hotel which overlook the harbour. There are also some boutique hotels in Valletta.
As to shipspotting sites , the whole of the bastions overlooking both harbours at Valletta are good sites, then there are our favourite sites for morning shooting, with the sun at your back at Senglea point and the surrounding bastions looking over the dockyard and the yacht marinas and Corradino Heights overlooking the smaller yard of Bezzina the inner part of Valletta Harbour. On the South side you can visit Marsaxlokk and Birzebbugia in Marsaxlokk Bay for the container ships at the Freeport.
If you travel to Gozo you can photo the ferries and other harbour cruise vessels plus large and small m/yachts.
Happy hunting Colwyn ,look us up at Senglea Point most mornings.
Best regards
Emmanuel.L.