The 34-year-old Henry, France's all-time leading scorer, now tops the salary table earning $5.6 million (4.5 euro) in 2012 playing for the New York Red Bulls.
The figure for total compensation includes salary and some bonus payments guaranteed over the life of a contract.
Henry's Red Bulls teammate Rafa Marquez of Mexico -- who like Henry joined the team in 2010 -- is second at $4.6 million.
Beckham, who ushered in the era of high-paid foreign imports in MLS when he first signed a five-year contract with the Galaxy in 2007, will make $4 million in total compensation this season, compared to the $6.5 million per year he made under his prior contract.
The 37-year-old midfielder inked a new two-year deal with the Galaxy in January, reportedly rejecting a rich offer from French club Paris Saint-Germain.
Beckham's teammate Robbie Keane of Ireland is fourth at $3.4 million, followed by the Galaxy's Landon Donovan and Toronto FC's Torsten Frings, both earning $2.4 million this season.
The remaining players whose wages top $1 million are Toronto's Julian de Guzman ($1.9 million) and Danny Koevermans ($1.6 million) and Portland Timbers striker Kris Boyd ($1.5 million).
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