ghegde,
both are good devices.
Cyclone IV is cosidered "more advanced" as it uses newer silicon process than the Spartan 3 series.
Cyclone IV is better comparable to Spatan 6.
But when shopping for an FPGA evaluation board - you must consider other factors that are just as (and sometimes more) important than the device maker and specific family.
Base your decision on what you need:
1. Number of easily reachable GPIOs.
2. Debug connectors (for example : RS-232 or USB to UART).
3. On board peripherials and connector ( for example : VGA ).
4. FPGA logic density.
5. On PCB memory (FLASH and RAM)
6. Fast signals (if needed)
7. Features that enhance debugability (simple switches and LEDs).
8. On PCB A/D and D/A
For a first board I'd buy either DE2 or Spartan 3A/3AN starter kit.
Both boards are great starters - you can't go wrong with these.