“I know I can look back on my time here and know that I gave absolutely everything I had to this club,” he told San Diego’s website.
“I played as if I was one of the fans and tried to bring that energy on to the pitch.
“To win their supporters player of the year in both my healthy season here is something that I will cherish.”
Overall, Morgan made 82 appearances – 73 of them starts – and provided 31 goals and 10 assists during his time with New York.
The former Celtic forward, who last played for Scotland against Finland in June 2024, now joins a side who were led by head coach Mikey Varas to a fourth-place finish overall in the MLS.
Sporting director Tyler Heaps told San Diego’s website: “Lewis is an attacker who can play across the front three and brings qualities that will add to our group in 2026.
“He’s proven he can contribute goals and assists in this league.”