The news this week in NY is focused on the budget deficit for the MTA. The NY Times City Room has a nice article about the current thinking of the Governor, the Mayor, and the various boards involved. I agree with this commenter that a toll on the inter-borough crossings (Brooklyn, Manhattan, and Williamsburg bridges) is a bad tax. This mainly lies around the issues that tolls are inefficient. 40% of the income would go to maintaining the toll. That doesn't include the increased waste caused by sitting in traffic, the BQE backing up, and Williamsburg being full of cars waiting to pay the toll.
The best solution is a gas tax. Increasing the gas tax would cost virtually nothing and it would raise money in a much more equitable way. The tax would ideally come from all the counties where the MTA operates. If that is not possible, the 5 boroughs should be where the tax is raised.
The underlying problem of inefficiency in spending is still to be addressed, but honestly, I'm not sure where this waste is. MTA workers may get paid slightly more than they should, but it's not over the top. Every year, the Post uncovers some $1M that was wasted, but that's the nature of a billion dollar operation. That's not waste, it's just organizational inefficiency - it can be battled but not defeated. The only area I see waste is in the bus system. On 23rd street, every morning, there are about a dozen buses pulling up every 5 minutes - each with just one or two passengers. I presume that most of the passengers were dropped off in midtown but if this is the case, the buses should terminate at midtown and the passengers should take the subway or a local bus. Otherwise, express busses that are terminating in Manhattan should accept local passengers while in Manhattan - that would be another good option to reduce waste.