Party's sitting Rajya Sabha MP Derek O'Brien, Sukhendu Sekhar Roy and Dola Sen were renominated by Banerjee for the elections scheduled for June 8.
Bhunia, a six-time Congress MLA from Sabang of West Midnapore district had joined the TMC last September.
Chhetri had lost the elections as a TMC candidate for the Kurseong Assembly constituency to GJM last year.
Naming the five candidates for the Rajya Sabha elections, Banerjee tweeted "My best wishes to all of them. Salute to Ma, Mati, Manush."
Elections to replace the retiring in the Rajya Sabha from three states will be held on June 8, the Election Commission has announced.