Tim Cahill is now the proud owner of the MLS record for fastest goal scored, and the Red Bulls are in control of the Supporters' Shield race.
Straight from the opening kick, Cahill chested down a long ball at the top of the Houston box and pounded a vicious volley into the net with only eight seconds gone.
Houston had chances to climb back into the game but couldn't find an equalizer before New York scored a second in the 65th. Sekagya latched onto a header from the top of the box and headed home to put the Red Bulls two goals up and salt away the win.
Bradley Wright-Phillips added a third goal 10 minutes later to put some padding on the score for New York, with the win taking the club back to the top of the race for the Supporters' Shield.
The result takes the Dynamo's playoff destiny out of the team's hands. Houston trails the New England Revolution on goals scored as the two sides head into the final week of the MLS season with the Dynamo in sixth place in the East and the Revs clinging to fifth and the final playoff spot.