This is the first I've heard of Joseph Clift, quoted in the news story as saying the new tunnels are more important than Portal Bridge; I'd be interested in knowing how the trains are supposed to get to the tunnels if something isn't done about Portal Bridge.
I suspect the idea is two-fold:
1) The talk is all about the tunnels failing sooner rather than later due to Sandy.
2) Worst case, I suppose you could still run trains to/from Seacacus if the Portal Bridge gets stuck open.
(and other than falling down, a Portal bridge outage is probably measured in hours or days, not months or years like a tunnel failure).