Sound-wise, it's always better to run everything through the receiver. It's also more convenient since you will only need to switch inputs on one device. Many TVs will not properly pass through the audio to the receiver, often reducing channels and quality in the process.
As far as input-lag, In my experience with various Onkyo models, the amount of lag added by the receiver is very minimal if any, to the point where it's imperceptible to me. Be sure you are selecting the game mode on the receiver just in case it reduces lag (though I suspect this is just sound-processing) and set your video processing for that input to "Passthrough" so the receiver is not trying to upscale or otherwise molest the signal. If you have any "A/V Sync" or other audio delay settings that try to delay the sound to match the video, you should probably turn those off as well.
You should be fine and you'll get better sound as a result.