Musumeci, who stands 6-foot-1 and weighs about 500 pounds, was arraigned in the employee parking lot after his attorney told Doyle it was impossible for his client to walk into the building and ride the elevator up to Doyle's third-floor courtroom.
Musumeci, of Centereach, pleaded not guilty.
Police say the charges come after a two-month investigation after officials from the Gibson Guitar Corporation of Nashville, Tennessee contacted police to say their logo was being put on other guitars.
Police say 15 guitars were seized at the music store yesterday and Musumeci turned over another 18 guitars from his home. Gibson will be examining the guitars for authenticity.