Well, buckle yourself in and prepare to take this all with a grain of salt. Again, these are suggestions, you're free to take them or leave them. I'm ignoring that these things can fly and just going for cities right there on the ocean. Especially ones with economic or military importance.

[hider=List of Cities]

[b]NORTH AMERICA[/b]
New York City/ Newark- Huge city, also the biggest port in the United States. Huge death toll and economic chaos to boot.

Houston- Fourth-largest city in the US, second-largest port. Same as above.

Boston- Sits right on the Atlantic, densely populated. 

Savannah, GA- Kind of a dark horse, but a VERY important port and a good-sized city. If the aliens in the movie were willing to attack Anchorage and Cabo, these guys could hit Savannah.

Quebec City- High population.

Havana- High population, national capital, not much exposure in media.

Norfolk/ Newport News/ Virginia Beach, VA- Important navy bases as well as heavily populated cities in their own right. 

Panama Canal Zone- Not a huge population, but would cause economic chaos. 

Panama City- Technically on the Pacific, but only ten minutes from the Atlantic. Huge city, plenty of skyscrapers.

[b]SOUTH AMERICA[/b]
Maracaibo- Big city in its own right and also a massive oil producer.

Caracas- Huge city, national capital.

Natal, Brazil- Huge city, center for oil industry.

Recife, Brazil- Huge city, medical hub.

Salvador, Brazil- Huge city.

Rio de Janeiro- One of the world's largest cities.

Sao Paolo- One of the world's largest cities, and ports. Capital of a powerful nation.

Montevideo- Large city, national capital.

Buenos Aires- One of the world's largest cities, capital of a powerful nation.

[b]EUROPE[/b]

Rotterdam- One of the world's busiest ports, an attack here would cause economic problems across the world.

Hamburg- Large city, busy port, naval bases.

Copenhagen/ Malmo- Large cities, Copenhagen is capital of Denmark.

Stockholm- Large city, national capital.

Helsinki- National capital, large city.

St. Petersburg- Huge city, one of the country's largest ports.

Edinburgh- Large city.

Liverpool- Large city, busy port.

Dublin- Large city, national capital.

Gibraltar- Important military bases.

Benidorm, Spain- Skyscrapers that would look good being knocked down.

Valencia, Spain- Huge city.

Barcelona- Huge city, important port.

Athens- National capital, huge city.

Istanbul- One of the biggest cities in the world.

[b]AFRICA[/b]

Luanda, Angola- National capital, huge city, important to oil industry.

Dakar, Senegal- Large city, national capital.

Lagos, Nigeria- One of the biggest cities in the world, important port.

Port Said, Egypt- One of the busiest ports in the world.

Monrovia, Liberia- Large city, national capital.

Accra, Ghana- Large city, national capital.

Cape Town, South Africa- Huge city, national capital, important port.
[/hider]