In former days, your configuration 1 would be the choice. This is because back then, most logic outputs (including these on a uC) could sink more current than they would source. Another reason to do so are integrated pull-up resistors, that some devices had (and some still have), so the LED would glow dark while the port pin isn't initialized yet. The 8051 family is a good example for that.
With most of todays uC, it just doesn't matter and it's up to your personal favour, since these output have similar to equal capabilities to source and sink. Beware of exceptions to this rule, always check the datasheets for hidden surprises ...