Thank you for your answer, Mykhailo.

These, specifically 3D-max, look like some of the more visually stunning options. However, I am not seeing the ability to attach data to objects as I would need (is that fair?). 

A professor has recommended me to check out "processing", which is a programming language with an awful name. Have you ever worked with this language? 

I am not sure if by "taking notes" you mean to add a certain comment to a specific portion of your 3D model. If that is the case, than in SolidWorks you can add a comment to a sketch or a model in the Feature Manager Design Tree. Hope this helps ;)

The best solution for editing detailed level might be a game engine like Unity or UE. An easy to handle WebGL alternative could be Sketchfab. Navigation and editing are quite restricted, but you can use simple annotations to move within the 3D model.

Edit: Before authoring the model can be created in a 3D app like Cinema 4D. It’s easy to learn, you can also attach notes to your model within the app.

https://skfb.ly/Np6y

I use Autodesk Maya to add detailed notes about object or scene in Attribute editor, or create script that pops up a window containing some information about the object. Whereas, to attach notes on an objects, you can use Maya's text annotations or can also create text objects and link them with object component to have them as renderable nodes for final output.

Cinema 4D offers an Annotation tag that can be attached onto any object.  It has user input options for a Textbox and a a URL.  I used an older version of this years ago to export some file formats that allowed you to click on the object to go to the link.  In C4D it had a little flag label sticking out of the object.  I'm sure many software packages offer such capabilities, and you could thus presumably annotate the final file directly once you learn the format or use a viewer such as webGL to trigger a label event upon rollover or click etc.