The FlynnStoned Cannabis Company, a dispensary in Syracuse, N.Y., is the size of a large clothing store. Its wooden front doors have iron handles with finials in the shape of cannabis leaves. Inside, nuggets of cannabis flower, infused candies and vaporizers are laid out in glass cases spread over two stories. A lounge under a skylight on the third floor hosts concerts and yoga classes.

It is, by nearly any measure, one of the success stories of New York’s nascent legal marijuana industry. And the man behind FlynnStoned, a 43-year-old high school dropout and roofing entrepreneur named Michael Flynn, appears poised to build a weed empire, with FlynnStoned dispensaries from Brooklyn to Buffalo.

But Mr. Flynn’s hard-charging approach has drawn ire from communities where he is seeking to open more stores. And a recent deal-making spree, in which he has cut branding agreements with dispensaries all over the state to use his name, has drawn the attention of regulators, who are investigating whether he is violating the spirit, and perhaps the letter, of the state’s legalization law.

“They’re trying to stick a pitchfork in me,” Mr. Flynn said.

Mr. Flynn, who has tattoos on his fingers that spell “HIGH VIDA,” is in some ways the type of person whom the state’s legalization efforts were intended to support. His conviction for marijuana possession 25 years ago put him at the front of the line for a state license to sell recreational cannabis products, part of New York’s effort to right the wrongs of the war on drugs.

And in some ways, the success of his business is a bright spot in the state’s troubled marijuana rollout. As others struggled to get off the ground, hamstrung by a combination of complex rules and a slow bureaucracy, FlynnStoned made $30 million in revenue in its first year.