I have started a CW answer, where various users can add players they find (or occasionally update numbers for active players). I guess in this way we can find at least an approximation of a complete list.
We could get very different numbers depending on which competitions we count (for example, all competitions including European cups, all domestic competitions including domestic cups and lower level leagues). To make this list correspond to the OP, let us only count top-level domestic leagues. (I.e., we don't count cups, only league matches in the top-level league.)
Players with 300 or more goals for a single team in a top-flight domestic league (European clubs)
- Lionel Messi (Barcelona/La Liga) 4741
- Uwe Seeler (Hamburger SV/Oberliga & Bundesliga) 4042
- Jimmy McGrory (Celtic Glasgow/Scottish League) 3953
- Josef Bican (Slavia Prague/Czechoslovak First League) 3954
- Ferenc Szusza (Újpest/Hungarian League) 393
- Gyula Zsengellér (Újpest/Hungarian League) 368
- Gerd Müller (Bayern Munich/Bundesliga) 365
- Ferenc Puskás (Budapest Honvéd/National Championship I) 352
- Albert De Cleyn (KV Mechelen/Belgian First Division) 3506
- Joseph Mermans (Anderlecht/Belgian First Division) 339
- Fernando Peyroteo (Sporting/Primeira Liga) 3296
- Eusébio (Benfica/Primeira Divisão) 317
- Cristiano Ronaldo (Real Madrid/La Liga) 311
- Dixie Dean (Everton/First Division) 3107
- Willy van der Kuijlen (PSV Eindhoven/Eredivisie) 308
Players marked in bold still play in the given club and competition.
1As of 7 August 2021
2404 goals for Hamburger SV, if we count both Oberliga and Bundesliga; 137 if we only count Bundesliga. (Oberliga was the highest level competition in the North of Germany before the foundation of Bundesliga.)
3395 according to stats at Wikipedia, 397 according to RSSSF.
4The number 395 is from Wikipedia. RSSSF lists separately 218 goals in Czechoslovak competitions and 232 goals in the era of Protectorate of Bohemia and Moravia. His stats at RSSSF are not broken down by the team, only total number of goals is given.
5377 according to Albert De Cleyn Wikipedia page, 350 according to RSSSF and Belgian Pro League Wikipedia page.
6330 according to RSSSF.
7308 according to RSSSF.
Sources