Don't know about Lionel. I mean, they slapped a "MTA Officially Licensed" logo on a New York Central starter set (as if it were a Grand Central tie-in).
Unsure about MTH either (other than re-issues). The economy's downturn has made it risky to do much in the way of new tooling. As far as newly-tooled rapid-transit models, I'd bet on a London Underground train before BART, only because the European 'O' models' sales haven't gone flat like those of US 'O'.
---PCJ