maxxyz says (post #1300) that 34A to 39 is currently free. Toll issues are complicated because the Thruway Authority also controls the barge canal.
On the 81 project, did the DOT ever look at just building a new beltway on the West side of Syracuse and tearing down the viaduct - in phases? I'm sure the East side work - rebuilding the interchanges between 81 and 481 (and adding lanes to 481/690) - will be expensive. Adding a West-side beltway would have to be cheaper than a tunnel - assuming eminent domain issues could be resolved.
Matt's CG post above has a cool DOT feature:
Geocortex Viewer for HTML5