Another option is from Borivali, come to Thane by road (via, Kashi-Mira, Ghodbunder) and take bus to Pune (from Vandana Talkies ST Stand, Thane).
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BEST, TMT buses ply between Thane & Borivali.
i think its neither tmt nor best, but msrtc b/w tna and bvi via ghodbunder