I'm currently working alone on a project that I intend to publish under the AGPL3+ license. I want to use parts of the Sympy source in it. The Sympy license says, that " Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.". Can I just put the GPL and this copyright notice at the beginning of the file and I'm good?
The Sympy licence you link to is actually three licences, all of which are slight variants of 3-clause BSD (BSD3), inasmuch as the authors have replaced "the author" in clause c with project-specific text. I'm not sure why they've done this, though it doesn't change anything.
It is pretty well established, not least by the FSF, and by custom and practice, that you can combine code licensed under BSD3 with code licensed under any version of the GPL, including (in your case) AGPLv3+. There is more argument about whether the resulting work must in its entirety be licensed under AGPLv3+ (as the AGPLv3 requires), or whether the BSD3 bits remain available under the terms of BSD3 in perpetuity. I have written about this elsewhere on SE, and I'm personally satisfied that the terms of the AGPLv3+ will cover the entire combined work. As you will see from the other answers to that question, this position is not universally held.
Nevertheless, you ask how to do it. AGPLv3 gives advice at the bottom about how to apply it to your code, so I assume you have read and followed that. This will have you add at the top a line which says
Copyright (c) 2019 Kryptomatrix
Then in each file which contains any sympy code at all, I would add the other copyright lines immediately below yours:
Copyright (c) 2006-2019 SymPy Development Team Copyright (c) 2013-2017 Sergey B Kirpichev Copyright (c) 2014 Matthew Rocklin
In these files, I would also below the AGPL header add a line that said
This file contains code derived from the sympy project, to which the following terms originally applied:
And then below that quote all three BSD3-type licences verbatim. That satisfies the requirement to reproduce the text, while making clear that it is now not the sole copyright licence applicable.