Clojure can utilize all libraries available for Java, and all invocations of those libraries will have the exact same speed any java application would have (Clojure itself isn't slow either, but that's a different topic).
I never attemped to actually use Mono, so please correct me if I'm wrong, but if I understood correctly, Mono has to duplicate all .NET frameworks, libraries and tools, which means Mono
a) is not complete (e.g. Silverlight, VisualStudio)
b) will hardly ever keep the pace of development of Microsofts implementation (simply due to resources).
Mono may be viable if you are happy with a subset of the .NET ecosystem, but I'd really feel more comfortable if I have access to all of Java with Clojure. Chances are you do need that library...
Mono can utilize all the libraries available for .Net, with a few exceptions (which are well known and documented on Mono's site here: http://www.mono-project.com/Compatibility).
Mono is a complete implementation of the C# specification, additionally, the Mono project has ported many .Net libraries.
Moonlight is the Mono version of Silverlight. Visual Studio is an IDE, and doesn't have anything to do with Mono vs .Net (in the same way IntelliJ IDEA has nothing to do with Java portability). You can write code in Visual Studio and compile it with Mono with no problems. You can also use MonoDevelop on OSX and Linux.
The time between Microsoft releasing new versions of .Net / C# and the Mono implementation is very small, usually weeks but sometimes only days. Unless you need to work on the bleeding edge right now, I don't think that it really makes much of a difference.
Yes, you can write C# in a way that isn't portable, especially if you use libraries that are OS specific. You can do that in Java as well (or any other language). Just look at all the libraries that require epoll or kqueue - those won't run on Windows no matter what language they were written in.
It's unfair to say that Mono requires you use a subset of the .Net ecosystem. If you want to write cross-platform code, you will always be constrained to a subset of the libraries.
C# is a nice language, especially with Linq (which is in Mono). You should spend a weekend with it sometime to form an opinion :D. MonoDevelop works fine on the mac and is free.
I never attemped to actually use Mono, so please correct me if I'm wrong, but if I understood correctly, Mono has to duplicate all .NET frameworks, libraries and tools, which means Mono
a) is not complete (e.g. Silverlight, VisualStudio)
b) will hardly ever keep the pace of development of Microsofts implementation (simply due to resources).
Mono may be viable if you are happy with a subset of the .NET ecosystem, but I'd really feel more comfortable if I have access to all of Java with Clojure. Chances are you do need that library...