This is very much an "it depends" kind of question; as posed there's no single "correct" answer.
Is the lengthy article something that users are likely to read continuously, from beginning to end? If so, intra-article navigation may not be necessary at all, and if included should be backgrounded rather than made persistently available so it doesn't interfere with that reading. Leading with a table of contents provides the user with an indication of the length and overall structure of what they're about to dive into, but there's no need in this case to constantly take up screen real estate with a lot of links the user is unlikely to follow mid-read.
Is it more of a reference-type article, which users are likely to select and read only the specific portions which interest them? If so, intra-article navigation is of paramount importance, but should probably be up front rather than paired with the text, and the article itself should probably be split into multiple literal pages rather than a single long scroll, to facilitate linking to / bookmarking of its individual components.
Is it something for which the full context of the article is necessary to understand any given portion, and users are likely to read in its entirety, but within which they are likely to want to skip around, comparing back to earlier sections as they go, skipping ahead to a glossary or data table, etc? In this case you may be best off with a single long-scroll page or separate pages with easily-available navigation, or even a nonlinear navigation structure based on sidebars, "footnote" popups, and so forth.
(Be wary of "fixed" navigation kept onscreen at all times, however: it can be a distraction to those who don't wish to use it, and when used carelessly can make portions of the navigation unreachable to some users (it's unfortunately common for fixed, unscrollable navigation to extend past the end of a small screen, for example.) Any navigation, whether intra- or inter-page, needs to be equally accessible on a small as on a large screen.)