Unless I'm mistaken... your IRA is funded by taxed income. 401K is pre tax (actually tax deferred). Thus, 401K may end up helping you by lowering your taxable income.
I do believe, however, you are allowed to put a certain amount into an IRA and deduct that (like 3K?)... so maybe you'd want to do both...
But definitely put money away in the 401K if possible - its amazing how fast it accumulates over time. I think the last time I saw that graph.... a 29 year old had to put twice as much than a 21 year old in order to come out even at 65 - IIRC.