There is a third option and that is to modulate the PWM frequency across a range around the centre frequency of 100kHz. There are a few chips that do this and this "spreads" the emissions around and can make passing the EMC testing easier. This is because the average time at one spot frequency is reduced and, in effect you are distributing emitted energy across a wider part of the spectrum. Some say it's a bit of a cheat but plenty of folk do it.
Any filtering you apply (sensible filtering of course) is going to help. I also found that a copper shield around the switching transformer also helped but there will be anecdotal evidence from several folk. I used a common mode choke and I believe this to be very important.
Choosing a higher frequency of 1MHz may not improve things - the switching rise times and fall times have to be so much sharper to get the same efficiency from the supply and this just pushes emissions to a different part of the spectrum.
Here is an article from MAXIM that explains how spread-spectrum modulation improves emissions in a class D audio amp. It's a rather approachable document and that is why I've linked it.
This document from TI is also very useful in that it takes you through how the labs measure emissions and tells you how the spread spectrum modulation helps.
The circuit below is a good example of using spread spectrum and generally I've found that Power Integrations (the company) provide really useful products and design help: -