The German national champion took advantage of his Lotto Belisol teammates' lead out as they protected him in the final corners leading to the sprint finish.
Greipel now lies second in the overall standings following Boom's second place finish in his home town Vlijmen. The Dutchman took the white race leader's jersey and now leads Greipel by one second.
Omega Pharma-Quick Step's Alessandro Petacchi continued his impressive comeback from injury by taking fourth spot, with Garmin-Sharp's Tyler Farrar in fifth.
Britain's Bradley Wiggins finished in a second group that crossed the line several minutes after Greipel due to a crash with six kilometres to go.
1 André Greipel (Ger) Lotto Belisol 2 Giacomo Nizzolo (Ita) RadioShack Leopard 3 Lars Boom (Ned) Belkin Pro Cycling 4 Alessandro Petacchi (Ita) Omega Pharma-Quick-Step Cycling Team 5 Alexander Porsev (Rus) Katusha 6 Tyler Farrar (USA) Garmin-Sharp 7 Jens Keukeleire (Bel) Orica-GreenEdge 8 Yauheni Hutarovich (Blr) Ag2R La Mondiale 9 Elia Viviani (Ita) Cannondale Pro Cycling 10 Christopher Sutton (Aus) Sky Procycling