A clinical fnish from Aguero after 16 minutes set City on their way, before he doubled his account six minutes after the break with a free header from David Silva's free-kick.
Ricardo Vaz Te sparked a West Ham fightback with a well-executed finish, but Silva's thumping strike sealed the points late on.
Most of the pre-match talk was of West Ham's continuing lack of strikers, with the returning Carlton Cole confined to the bench for the 90 minutes, and the progress of the youngster Ravel Morrison.
However, a combination of Aguero, Silva, and some poor defending cost the Hammers all three points as Man City moved up to fourth in the table.
Manuel Pellegrini's side settled quicker, taking control of the middle of the park, setting the tempo without creating many clear-cut opportunities early on.
Aguero soon left his first mark on the contest however, and sped clear to finish off a well-worked move after 16 minutes.
The half went on with several more City opportunities going begging, and West Ham struggling to impose themselves.
After the break, Aguero doubled his tally after some woeful Hammers defending, finding himself unmarked from a Silva free-kick.
Sam Allardyce had clearly urged his side to up the tempo however, and West Ham soon fought back. Good work from wonderkid Ravel Morrison allowed Vaz Te to hook the ball over Joe Hart in the 58th minute.
West Ham's lack of an out-and-out striker was telling though, with the likes of Noble and Nolan not able to fully fill the gap left by an injured Andy Carroll and an unfit Cole.
City eventually finished off a spirited home side with Aguero turning provider for Silva with a lovely backheel, before Silva's unstoppable effort into the top corner.
It was a welcome victorious away day for Pellegrini as his side kept up the pressure on the top sides.
- 22 Jääskeläinen
- 20 Demel (O'Brien - 65' )
- 08 Rat
- 16 Noble
- 05 Tomkins
- 02 Reid
- 23 Downing
- 04 Nolan Booked (Petric - 83' )
- 21 Diamé
- 15 Morrison
- 12 Vaz Te (Jarvis - 65' )
- 01 Hart
- 02 Richards
- 22 Clichy Booked
- 42 Yaya Touré
- 14 Javi García
- 33 Nastasic
- 08 Nasri (Milner - 74' )
- 25 Fernandinho
- 16 Agüero (Jovetic - 82' )
- 09 Negredo (Kolarov - 66' )
- 21 Silva Booked