I'm not sure it would actually work against moving monitor - even in the river. As i recall, there is no examples of moving ships being sucsessfully attacked by the spar torpedo boats. Moreover, i could recall the russian-turkish engagemen on Danube in 1878, when a couple of russian torpedo launches attacked the turkish monitor. She simply go away from them, firing grapeshots and shrapnels, and sending crewmens with rifles on the turrets.
I think, the "Onondaga" would do something like that. She would place one gunboat nearby to screen her, and user riflemens on the turret roofs to make things difficult for the torpedo boats. Also, there is "Spuyten Duyvil" nearby, who could charge the confederacy ironclad - and due to her armor, she seems to have much better chances to achieve hit than usual torpedo boat.
So, I think the best strategy for Union would be to charge the "Spyuten Duyvil" toward the Confederacy ironclads, to keep them away - and screen the "Onondaga" with the gunboats. It should gave enough time to deal with torpedo boats, that wouldn't have the ironclads cover.