Does a T1135 need to be filed if the market value is over $250,000 but adjusted cost basis is under $100,000?

Yes. As long as you met the reporting requirement threshold of $100,000 at any time in the year, you must report on Form T1135 all specified foreign properties held during the year, even if you sold any or all of the property before the end of the year

Here are additional resources from CRA talking about T1135

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By met the threshold, is that $100k in cost basis, or $100k in market value?

This is from the guide:

Is the $100,000 threshold based on the fair market value of the property?

No, it is based on the cost amount. The cost amount is defined in subsection 248(1) of the Income Tax Act and generally is the adjusted cost base and not the fair market value.