Sounds like a difficult project. The hardest thing in mixed signal design is to keep the digital noise out of your analog components. I can give you a few hints, but this really requires a good board layout and much experience to do really well.
1) Use linear power supplies and make the supplies for the analog section separate from the digital power. Separate analog and digital circuitry on your board.
2) Edge times on signals is the most important for noise. Altera has programmable slew rates, current and source termination. Use them all. I really recommend using small value resistors like source termination to control edge times. It also provides some isolation from your analog circuitry.
3) The jitter on your oscillator will drive the noise flow of your design. Buy a very low noise
oscillator, and use a ferrite bead and caps to isolate the power. It is a noise source. Also use low noise buffer to send oscillator to all of your converters.
4) The PLL's in the FPGA will be all over your system for noise. Make sure the power for these is also isolated like the oscillator, and better yet try not to use them in your design.
5) You can use the memory tool function in Quartus to capture the ADC data for evaluation. Analog devices has a nice tool for evaluating your ADC performance.
6) Make sure that all analog signals are over the analog ground plane. Make sure that the digital control signals enter the analog circuitry at one point for each of the converters.
7) Use signal integrity tools if you have them. Otherwise it may require several board spins to achieve the required noise floor.