Most MLB home runs by individuals by year.

1916-2018

Ties:

Query3

yearID	Num
1916	3
1917	2
1918	2
1923	2
1931	2
1935	2
1947	2
1948	2
1952	2
1967	2
1982	2
1987	2
1991	2
1993	2
2003	2

Players leading multiple times 1916-2018:

Query2

playerID	Num	First	Last	HRmax	HRmin	YearFirst	YearLast	FirstOfname
ruthba01	11	Babe	Ruth	60	11	1918	1931	Boston Red Sox
kinerra01	6	Ralph	Kiner	54	37	1947	1952	Pittsburgh Pirates
schmimi01	6	Mike	Schmidt	48	31	1974	1983	Philadelphia Phillies
foxxji01	4	Jimmie	Foxx	58	35	1932	1939	Philadelphia Athletics
killeha01	4	Harmon	Killebrew	49	44	1963	1969	Minnesota Twins
mcgwima01	5	Mark	McGwire	70	49	1987	1999	Oakland Athletics
gehrilo01	3	Lou	Gehrig	49	46	1931	1936	New York Yankees
greenha01	3	Hank	Greenberg	58	36	1935	1946	Detroit Tigers
mizejo01	3	Johnny	Mize	51	40	1940	1948	St. Louis Cardinals
mayswi01	3	Willie	Mays	52	49	1955	1965	New York Giants
rodrial01	3	Alex	Rodriguez	57	47	2002	2007	Texas Rangers
willicy01	2	Cy	Williams	41	12	1916	1923	Chicago Cubs
roberda01	2	Dave	Robertson	12	12	1916	1917	New York Giants
hornsro01	2	Rogers	Hornsby	42	39	1922	1925	St. Louis Cardinals
willite01	2	Ted	Williams	37	36	1941	1942	Boston Red Sox
matheed01	2	Eddie	Mathews	47	46	1953	1959	Milwaukee Braves
bankser01	2	Ernie	Banks	47	41	1958	1960	Chicago Cubs
benchjo01	2	Johnny	Bench	45	40	1970	1972	Cincinnati Reds
stargwi01	2	Willie	Stargell	48	44	1971	1973	Pittsburgh Pirates
cansejo01	2	Jose	Canseco	44	42	1988	1991	Oakland Athletics
fieldce01	2	Cecil	Fielder	51	44	1990	1991	Detroit Tigers
gonzaju03	2	Juan	Gonzalez	46	43	1992	1993	Texas Rangers
bondsba01	2	Barry	Bonds	73	46	1993	2001	San Francisco Giants
howarry01	2	Ryan	Howard	58	48	2006	2008	Philadelphia Phillies
bautijo02	2	Jose	Bautista	54	43	2010	2011	Toronto Blue Jays
davisch02	2	Chris	Davis	53	47	2013	2015	Baltimore Orioles

Mark McGwire actually led five times. In 1997 he played for Oakland and St. Louis and hit 58 home runs but did not lead either league. Ken Griffey got credit in 1997 with 56 home runs, his only time leading MLB.

Notable sluggers who led MLB only once:
1956 Mickey Mantle 52
1957 Hank Aaron 44
2009 Albert Pujols 47

Obviously, it becomes more difficult in more recent seasons because there are more teams and more players.

Teams with players leading multiple times 1916-2018 and most recent and first player:

Query1

franchID	Num	LastOfname	HRmax	HRmin	YearFirst	YearLast	theLast1	theLast2	theFirst1	theFirst2
NYY	17	New York Yankees	61	12	1916	2007	Alex	Rodriguez	Wally	Pipp
SFG	11	San Francisco Giants	73	12	1916	2001	Barry	Bonds	Dave	Robertson
PHI	11	Philadelphia Phillies	58	12	1917	2008	Ryan	Howard	Gavvy	Cravath
CHC	9	Chicago Cubs	56	12	1916	2000	Sammy	Sosa	Cy	Williams
OAK	9	Oakland Athletics	58	11	1918	2018	Khris	Davis	Tillie	Walker
BOS	8	Boston Red Sox	46	11	1918	1984	Tony	Armas	Babe	Ruth
DET	8	Detroit Tigers	58	34	1935	2012	Miguel	Cabrera	Hank	Greenberg
PIT	8	Pittsburgh Pirates	54	37	1947	1973	Willie	Stargell	Ralph	Kiner
STL	6	St. Louis Cardinals	70	39	1922	2009	Albert	Pujols	Rogers	Hornsby
ATL	5	Atlanta Braves	51	28	1945	2005	Andruw	Jones	Tommy	Holmes
BAL	5	Baltimore Orioles	53	40	1966	2016	Mark	Trumbo	Frank	Robinson
TEX	5	Texas Rangers	57	43	1968	2003	Alex	Rodriguez	Frank	Howard
CIN	4	Cincinnati Reds	52	40	1954	1977	George	Foster	Ted	Kluszewski
MIN	4	Minnesota Twins	49	44	1963	1969	Harmon	Killebrew	Harmon	Killebrew
TOR	3	Toronto Blue Jays	54	40	1986	2011	Jose	Bautista	Jesse	Barfield

The New York Mets have never had a player lead MLB in home runs in a season but rookie Pete Alonso currently leads in 2019 with 47. But he won't be the first rookie. Oakland's Mark McGwire led the AL and tied for the most in 1987 with 49; Cub Andre Dawson led the NL also with 49 in 1987. And the rookie record for home runs was set in 2017 by Yankee Aaron Judge, who led the AL with 52 but was second to NL leader Giancarlo Stanton of Miami who hit 59.