I don’t know about Notes alternatives offhand.
But I do know of a few ways to make Notes easier to work with in ID and IC. “Not being able to find them” is a common complaint for sure!
Solution 1
In both ID and IC, modify the Links panel so that it shows a count of Notes inside linked ICML files. (The ICML files appear in the Links panel). Links panel menu > Panel options > Show in column, and check the “# of Notes” attribute (scroll all the way down the list of attributes). Save the modified Links panel in a custom workspace so resetting the workspace doesn’t clear out your changes. There are no InCopy workspaces that include the Links panel, but it does have the pael. Just add it to the workspace’s dock from Window > Links.
Now, ID and IC users just need to open the Links panel to see where the notes are. Clickin the page number in the Links panel will jump them to the story where there are notes.
Solution 2
Install Rorohiko’s free script, ShowNotes.jsx.
https://www.rorohiko.com/wordpress/dont-let-adobe-indesign-incopy-notes-go-unnoticed/
Put this in the Scripts > startup scripts folder (create a “startup scripts” folder by hand if there’s not one there already) for each app that wants one, ID and/or IC. Also put the same script in the Scripts > Scripts panel folder in the User settings so it appears in the Scripts panel. Restart ID and IC and open a file with notes.
The ShowNotes startup script does a quick scan of every file you open in those programs to check for the presence of Notes. If it finds some, it says “there are Notes in this file” in an alert. Clicking OK to close the alert then jumps you to the first note, zoomed in so you can see where it is, and opens the Notes panel. From there you’d click the Next/Previous Note buttons in the panel to find the other notes.
And, at any time you can run the script from the Script panel to run the same check again.
Solution 3
Purchase vJoon’s Notes Manager plugin. It works in both ID and IC but only up to ID 2020, haven’t seen an update yet for 2021. There is a free 30 day demo, after that it’s around $100 a seat.
https://vjoon.com/what-we-offer/generic-adobe-plug-ins/
Install the plugin and restart. When you open a doc that has Notes, open the Notes Manager from the Window menu and you’ll see a interactive dialog box listing all the notes, let you sort, print, navigate, read, all sorts of stuff.
Hope that helps a bit!
AM