If it better to siphon or funnel? The answer is: yes.
If we're talking about fresh wort, the answer is funnel. You need to add oxygen back into that wort to replace all that was removed from the boil. Then again, if you're using a counterflow chiller (CFC) you will either siphon or pump the wort through it.
Any time after that, you want to siphon. This reduces the chance of oxidation, which is dangerous after fermentation has started.
To summarize:
From the kettle to the fermenter: Funneling is generally preferred, since oxygen is critical at this point. If you use a wort wizard, a CFC, an aeration stone, or other device to reintroduce oxygen, it doesn't really matter.
After introduction of yeast: Siphon. Bottom line.
