Gov. Andrew Cuomo ordered the cash-strapped MTA to waste as much as $30 million on his latest vanity project — retiling two city tunnels in the state’s blue-and-gold color scheme — instead of using the dough for desperately needed subway repairs, The Post has learned. The boondoggle began soon after the taxpayer-funded agency ordered white tiles to reline the Brooklyn-Battery and Queens-Midtown tunnels after Superstorm Sandy, documents show. The governor got wind of the plan — and insisted that the cash-strapped transit agency add stripes of blue and gold, thinking nothing of the additional $20 million to $30 million cost,...