Crossrail is not directly comparable, for starters, only 21km of crossrail is underground; Most of it's 118km length is above ground so the per-km cost of the below ground sections get averaged out over the above ground sections.

This section of the 2nd Avenue subway (it's just 2.7km long) is deep under Manhattan itself. To get a comparison on cost you would have to only compare only the section of crossrail running under central london itself.