They have very slightly different meanings.
Muddle through - to do something or live in a disorganized way, with no plan.
Getting by - living and possibly succeeding, but not in a spectacular way.
Scrape by - living and making a living, but just barely, with very little extra money, if any.
"Just getting by" or "just barely getting by" = "scraping by"
Even more dramatic - "Hanging on by my fingernails" = very close to failure or going broke.