Hi,
Assuming you are using SOPC builder, I think you can easily do it using the 'system-console', a new Altera tool available since Quartus 8.0. Be aware that you have to know TCL scripting, at least a little.
See the NIOS wiki :
http://nioswiki.jot.com/wikihome/systemconsole There are some examples. All you have to do is to have an JTAG avalon master (i.e NIOS processor+debug module or the new Altera SOPC JTAG avalon master component) in your design. Then you have some basic TCL command which allows read/write accesses on the Avalon bus, at a user specified adress.
I personnally use the system console for programming in-system an MSP430 (see here (
http://nioswiki.jot.com/wikihome/system%20console%20-%20msp430)) and a Xilinx CPLD on my custom board.
Great tool IMO.
Regards.