Which of the sentences is correct Mary as well as Tom is tall and Mary as well as Tom are tall?

The singular subject is Mary, so you use the singular verb "is." Tom is in a separate clause, not a compound subject. "Mary, as well as Tom, is tall."

This phrasing would not be used in English, however. The expression would normally be "Tom is tall, and Mary is as well." Introducing the information that Tom is tall and that Mary is tall should be in two separate independent clauses. Unless you just say "Mary and Tom are both tall."