Is there a 3-dimensional airspace viewer? I am using SkyVector to have an idea of what the airspace looks like in terms of waypoints and airways.

I was wandering if anybody knows a website that displays such information but in 3D (or 3D + time) in order to navigate through the airways and check out some information as viable flight levels or altitude constraints.

I am imaging of a website/software that allows to navigate like on google earth or cesium and see what the airspace is like (qualitatively at least).
You can download Google Earth airspace files for most countries, and move through them in 3D to explore what they would look like for various areas.  For example, you could see where you would be "under" a Class B shelf, or where you might navigate to avoid B/C/D airspace and "surface airport E airspace" (if you're flying an ultralight, for example). 

These files can be downloaded from 3dairspace.org.uk

Here is a screenshot I just captured of the Seattle Class B, looking northwest from the southeast corner.