I'm not sure which route is better to be honest, but I'm one of the rarer people who went the small company route. My undergrad internships and five years of pre-MBA full-time experience were all with the same small company (80-200 people).
I attended Kellogg, where I was definitely in the minority of people from small firms. Most commonly, other students from small firms were from VC/PE, where small in terms of the number of employees is typical.
As you alluded to, I was able to make a significant impact on the small company I worked for, which translated well into B school essays and interviews. The thing is, that you could probably make a similar impact in a small-ish component of a big company (a division, business unit, department, group, etc.), which would give you that impactful experience that B schools like but with a brand name organization. So that is probably the ideal situation if you think you can manage it, which many students at top schools have.
When it comes to small company experience, I think it is especially important for the work to have been meaningful beyond just trying to make money. This can make up for some of the lack of prestige.
I just started my post-Kellogg career.....at a massive company.