Brigadier General Meagher commanded the 69th New York Infantry (the Irish Brigade) during the Civil War. His brigade sustained the third most combat dead in all the Union's forces. He fought in many important battles like Bull Run (not as a brigadier general) and Gettysburg. From what I have read and heard he was not a well liked man and had been viewed by some as a poor military leader. I have also heard that there was a possibility that he was murdered when someone pushed him off a boat while he was drunk and resulting in him drowning. This is most likely a rumor. There are many critics and rumors surrounding him and I just wanted to see what people with knowledge had to say about it. Thanks.
There's a pretty significant difference between being seen as a bad military leader and being thought of as a jerk and/or drunk. It seems like Meagher was the latter in his time, so his detractors liked to also accuse him of incompetence. There were rumors of his drunkeness during battle and in general, which may be factual. But, like William McFeely theorizes about Grant's alcohol abuse, Meagher may have used alcohol to ease his depression (which, considering how many men he lost, would not surprise me). It's also possible he didn't drink all that much compared to others, but that people perceived the Irish as heavy drinkers, so if they didn't like this guy it wasn't an unbelievable accusation to throw around.
Based on the little research I've done on Meagher (which is... um... meager...^*), I have a feeling he was simply ill and fell (he was having health issues), or that he committed suicide due to his ill health and financial woes. In The Irish General: Thomas Francis Meagher by Paul Wylie, he mentions the latter idea, says that the barber on the steamship claimed to witness someone intentionally jumping off the boat, but concludes that this is unlikely since Meagher was so religious and would have believed suicide was a sin. Still, I believe it's more likely than him being murdered. Drunkeness may be possible, but I doubt murder.
In summary, he is widely regarded as a competent military leader. Criticisms seem to be strictly personal and based on possible behavioral infractions as opposed to incompetence.
I hope this helps. If you haven't already, check out Wylie's book (2012), along with Thomas Francis Meagher: the making of an Irish American by John Hearne and Rory Cornish (2006) and Thomas Francis Meagher and the Irish Brigade in the Civil War by Daniel Callaghan (2006) to get some info on modern interpretations of Meagher's life.
^*I'm ^sorry. ^I ^had ^to. ^Except ^it's ^not ^even ^pronounced ^that ^way ^so ^I'm ^extra ^sorry.