Figured out that the legend wasn't being extracted because the legend.position was set to "bottom".

To obtain the legend when legend.position = "bottom" use cowplot::get_plot_component(legendplot,"guide-box-bottom") rather than cowplot::get_legend(legendplot)

Change the value guide-box to one of the following values to match the position supplied in theme(legend.position="") if you aren't using the default legend.position:

1. guide-box-right when legend.position="right",
2. guide-box-left when legend.position="left",
3. guide-box-bottom when legend.position="bottom",
4. guide-box-top when legend.position="top",
5. guide-box-inside when legend.position="inside"

library(cowplot); library(patchwork); library(grid); library(tidyverse)

#Data to create legend
legend_data <- data.frame(
  julian = 299:366,
  PM25 = c(3.4,1.3,1.2,1.2,0.4,3.4,1.0,0.8,0.3,13.5,0.9,5.3,4.4,3.4,98.6,0.7,350.6,0.8,0.3,0.9,0.9,4.1,0.7,0.3,0.4,2.1,1.4,5.2,4.2,3.9,1.4,0.8,0.7,0.8,0.3,1.9,0.8,0.7,1.2,1.7,67.9,3.8,6.1,5.9,225.3,0.7,0.3,0.6,2.9,37.5,1.1,33.2,0.9,1.5,1.1,0.8,1.5,0.8,2.2,4.6,1.2,1.0,3.3,0.9,0.9,4.6,1.2,2.8),
  site_name = "community 1"
  )
legend_data$AQI <- case_when(
  legend_data$PM25 <= 9.0 ~ "1",
  legend_data$PM25 >= 9.1 & legend_data$PM25 <= 35.4 ~ "2",
  legend_data$PM25 >= 35.5 & legend_data$PM25 <= 55.4 ~ "3",
  legend_data$PM25 >= 55.5 & legend_data$PM25 <= 125.4 ~ "4",
  legend_data$PM25 >= 125.5 & legend_data$PM25 <= 225.4 ~ "5",
  legend_data$PM25 >= 225.5 ~ "6",
  TRUE ~ NA_character_
)

#Create plot
legendplot <- ggplot(legend_data, aes(x=julian, y=AQI, fill=AQI)) +
  geom_tile() +
  scale_fill_manual(
    values = c("green", "yellow", "orange", "red", "purple", "maroon"),
    labels = c("1" = "Good", "2"="Moderate", "3" = "Unhealthy for\nSensitive Groups", "4" = "Unhealthy", "5" = "Very Unhealthy", "6" = "Hazardous")
  ) +
  theme(legend.position = "bottom")
legendplot

#Extract legend
legend<-cowplot::get_plot_component(legendplot,"guide-box-bottom") 
grid.newpage()
grid.draw(legend)