Game: NBA 2K9
It's a real toss-up for Amar'e Stoudemire's best year in the NBA 2K franchise. He had a great year in 2004-05 and was mega-nice in NBA 2K6, but Stoudemire in NBA 2K9 was probably at his peak as far as video game form is considered.
Always a better rebounder on the virtual hardwood than in real life, Stoudemire had a career year in 2007-08, posting career highs in Player Efficiency Rating (27.6), win shares per 48 (.262), true shooting percentage and effective field goal percentage (.656 and .592) and points-per-36-minutes (26.7). His success that season paved the way for his 94 rating in NBA 2K9, plus the series' offensive pick and roll game was at or near its peak, allowing for fantastic finishes on dishes from Steve Nash (or whatever point guard you wanted to pair him with).
Injuries would eventually strip Stoudemire of his terrific athleticism, but in NBA 2K9 he was at his digital peak.