Companies like Rigol and Siglent seem to add "counters" to their other products but these are rather low spec. For instance the Rigol one is 12 digits but the accuracy is around 7 digits and it works in binary rather than decimal mode so the lower digits jump around.
I have the TTi 930 which I'm happy with as it is reasonably priced, does reciprocal counting, is 10 digits, allows an external reference and can be controlled over usb. It
also doesn't stop the counting when producing a measurement so you can get a constant stream of results over usb (or on the display).
But it doesn't do statistics directly - you would need to do this on a controlling pc (easy to do if you can write your own software or are willing to copy terminal output into a spreadsheet). It also doesn't seem to talk to Windows 7 64bit - I run mine from an IBM Thinkpad running Windows XP. Also the display is not backlit so is not as easy to see as one which is.
The clock is 50MHz so the resolution is 20 nsecs but you say you are only interested in subMHz signals. At the lower end it goes down to 0.01Hz which I find useful for looking at 1pps signals from a GPS module.
There does seem to be a bit of a gap in the counter market between 6/7 digit counters which are not much better than the ones built into a lot of scopes and other instruments, and the much more sophisticated and expensive Agilent offerings. To some extent TTi fit in there.